Comparative analysis of protein domain organization

We have developed a set of graph theory-based tools, which we call Comparative Analysis of Protein Domain Organization (CADO), to Survey and compare protein domain organizations of different organisms. In the language Of CADO, the organization of protein domains in a given organism is shown as a domain graph in which protein domains are represented as vertices, and domain combinations, defined as instances of two domains found in one protein, are represented as edges. CADO provides a new way to analyze and compare whole proteomes, including identifying the consensus and difference of domain organization between organisms. CADO Was Used to analyze and compare >50 bacterial, archaeal, and eukaryotic genomes. Examples and overviews presented here include the analysis of the modularity of domain graphs and the functional Study of domains based oil the graph topology. We also report oil the results of comparing domain graphs of two organisms, Pyrococcus horikoshii (an extremophile) and Haemophilus influenzae (a parasite with reduced genome) with other organisms. Our comparison provides new insights into the genome organization of these organisms. Finally, we report oil the specific domain combinations characterizing the three kingdoms of life, and the kingdom Signature domain organizations derived from those specific domain combinations.